Biblioteki

Kod wyliczający wykorzystane biblioteki.

#devtools::install_github("tidyverse/readr")
library(readr)
#devtools::install_github("hadley/dplyr")
library(dplyr)
#devtools::install_github("ropensci/plotly")
library(plotly)
#devtools::install_github("tidyverse/ggplot2")
library(ggplot2)
#devtools::install_github("topepo/caret/pkg/caret")
library(caret)
#devtools::install_github("haozhu233/kableExtra")
library(kableExtra)
#devtools::install_github("tidyverse/magrittr")
library(magrittr)

#Paczki do caret :
#install.packages("randomForest")
#library(randomForest)
#install.packages("e1071")
#library(e1071)

Powtarzalność eksperymentu

Kod zapewniający powtarzalność wyników przy każdym uruchomieniu raportu na tych samych danych.

set.seed(2157)

Wczytywanie danych

Kod pozwalający wczytać dane z pliku.

all_summary <- read_delim("all_summary.csv", delim = ";", trim_ws = TRUE, comment = "")

Czyszczenie danych

Kod usuwający z danych wiersze posiadające dane wartość zmiennej res_name.

to_remove = c('UNK', 'UNX', 'UNL', 'DUM', 'N', 'BLOB', 'ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLN', 'GLU', 'GLY', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'MSE', 'PHE', 'PRO', 'SEC', 'SER', 'THR', 'TRP', 'TYR', 'VAL', 'DA', 'DG', 'DT', 'DC', 'DU', 'A', 'G', 'T', 'C', 'U', 'HOH', 'H20', 'WAT')
all_summary %<>% filter(!(res_name %in% to_remove))

Przetwarzanie wartości pustych

Kod przetwarzający brakujące dane.

all_summary %<>% filter(!is.na(res_name))

Statystyki

Sekcja podsumowująca rozmiar zbioru i podstawowe statystyki

Rozmiar zbioru

Liczba kolumn

ncol(all_summary)
## [1] 412

Liczba wierszy

nrow(all_summary)
## [1] 591042

Statystyki

kable(t(do.call(cbind,lapply(all_summary, summary)))) %>%
  kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
  scroll_box(width = "100%", height = "600px")
Min. 1st Qu. Median Mean 3rd Qu. Max. NA’s
blob_coverage 575726 character character 575726 character character 575726
res_coverage 575726 character character 575726 character character 575726
title 575726 character character 575726 character character 575726
pdb_code 575726 character character 575726 character character 575726
res_name 575726 character character 575726 character character 575726
res_id -62 301 501 779.011967757066 999 9999 96
chain_id 575726 character character 575726 character character 575726
blob_volume_coverage 0.02004008016 0.504122352125 0.728749034 0.669962213490053 0.8703854008 1 0.02004008016
blob_volume_coverage_second 0 0 0 0.0193655752498971 0 0.9988751406 0
res_volume_coverage 0.001883948757 0.24625367585 0.4570532077 0.495926068892134 0.705417299775 1 0.001883948757
res_volume_coverage_second 0 0 0 0.06658263737737 0 1 0
local_res_atom_count 1 4 6 14.1170278917402 20 178 1
local_res_atom_non_h_count 1 4 6 13.7714537818337 20 111 1
local_res_atom_non_h_occupancy_sum -7.38 4 6 13.3183036461789 18.65 111 -7.38
local_res_atom_non_h_electron_sum 3 30 52 102.040731181152 137 1848 3
local_res_atom_non_h_electron_occupancy_sum -45.91 29 48 97.9419663451017 129 858 -45.91
local_res_atom_C_count 0 0 3 7.90501210645342 10 84 0
local_res_atom_N_count 0 0 0 1.21496336799102 1 28 0
local_res_atom_O_count 0 1 3 3.84094517183521 5 61 0
local_res_atom_S_count 0 0 0 0.22136050829735 0 13 0
dict_atom_non_h_count 1 4 6 14.1079280137555 20 128 11007
dict_atom_non_h_electron_sum 3 30 50 104.522504112665 138 1223 11007
dict_atom_C_count 0 0 3 8.05252169663142 10 93 11007
dict_atom_N_count 0 0 0 1.19241250958441 1 28 11007
dict_atom_O_count 0 1 3 4.05049591035542 6 55 11007
dict_atom_S_count 0 0 0 0.220739872396714 0 13 11007
skeleton_data 575726 character character 575726 character character 575726
skeleton_cycle_4 0 0 0 0.372863132809705 0 2792 0
skeleton_diameter 0 2 13 24.4203110507429 33 671 0
skeleton_cycle_6 0 0 0 0.0127751743016643 0 150 0
skeleton_cycle_7 0 0 0 0.00427112897454692 0 54 0
skeleton_closeness_006_008 0 0 0 2.61396740810733 0 417 0
skeleton_closeness_002_004 0 0 0 0.0853513650590733 0 907 0
skeleton_cycle_3 0 0 0 0.0562194516141359 0 957 0
skeleton_avg_degree 0 1.333333333 1.875 1.57384315293755 1.962962963 6.458598726 0
skeleton_closeness_004_006 0 0 0 0.945828397536328 0 492 0
skeleton_closeness_010_012 0 0 0 3.52082240510243 0 779 0
skeleton_closeness_012_014 0 0 0 3.27787523926312 0 2579 0
skeleton_edges 0 2 14 35.8367313617936 40 9934 0
skeleton_radius 0 1 7 12.5078370613799 17 336 0
skeleton_cycle_8_plus 0 0 0 0.190852940461261 0 1863 0
skeleton_closeness_020_030 0 0 0 5.31210332692982 1 1009 0
skeleton_deg_5_plus 0 0 0 0.148687049047637 0 2998 0
skeleton_closeness_016_018 0 0 0 2.25168917158509 0 434 0
skeleton_closeness_008_010 0 0 0 3.5107273251512 0 304 0
skeleton_closeness_018_020 0 0 0 1.75372312523666 0 569 0
skeleton_average_clustering 0 0 0 0.00012396244422612 0 0.4666666667 0
skeleton_closeness_040_050 0 0 0 1.83978316073966 1 572 0
skeleton_closeness_014_016 0 0 0 2.85511858071374 0 129 0
skeleton_center 1 1 1 1.6184278632544 2 251 1
skeleton_closeness_000_002 0 0 0 0.112369425733769 0 204 0
skeleton_density 0 0.02571785268 0.09090909091 0.218411095861248 0.25 1 0
skeleton_closeness_030_040 0 0 0 2.83986827067042 1 864 0
skeleton_deg_4 0 0 0 0.120800519691659 0 228 0
skeleton_deg_0 0 0 0 0.111071933523933 0 1 0
skeleton_deg_1 0 2 2 3.24242087381845 3 85 0
skeleton_deg_2 0 1 12 30.5136366952335 35 877 0
skeleton_deg_3 0 0 0 2.00964695011168 2 157 0
skeleton_graph_clique_number 1 2 2 1.89525572928789 2 5 1
skeleton_nodes 1 3 15 36.1462640214269 41 3801 1
skeleton_cycles 0 0 0 0.690467340366772 0 6134 0
skeleton_cycle_5 0 0 0 0.0534855122054589 0 320 0
skeleton_closeness_050_plus 0 0 3 5.22703681959821 11 310 0
skeleton_periphery 1 2 2 2.00518649496462 2 101 1
local_volume 49.248 212.976 347.2 861.32750772416 797.04 90952.512 49.248
local_electrons 0.01170493793 3.45070153825 7.851201172 17.828009979626 19.90227051 442.4445 0.01170493793
local_mean 0.000114725 0.012078 0.01859395 0.0235338288678278 0.0285545 0.426442 0.000114725
local_std 0.000660591 0.06827275 0.09843535 0.122630826234582 0.143231 1.95956 0.000660591
local_min 0 0 0 0 0 0 0
local_max 0.0045201 0.5650945 0.888857 1.35413959116681 1.50644 44.6336 0.0045201
local_max_over_std 2.836182117 5.23372314075 7.2410710645 9.76688605021531 11.2927055825 173.2519886 2.836182117
local_skewness 0.001174014706 0.120711275325 0.17421898725 0.222862932953116 0.25619059375 4.035154736 0.001174014706
local_cut_by_mainchain_volume 0 0 0 0.365240562350841 0.024 53.504 0
local_near_cut_count_C 0 0 2 4.38413933016748 6 163 0
local_near_cut_count_other 0 0 0 0.0121602984753164 0 14 0
local_near_cut_count_S 0 0 0 0.123291287869577 0 15 0
local_near_cut_count_O 0 0 1 2.0936695580884 3 76 0
local_near_cut_count_N 0 0 1 2.16578546044473 3 41 0
part_00_shape_segments_count 0 5 25 340.913674213081 144 114577 0
part_00_density_segments_count 0 5 25 340.913674213081 144 114577 0
part_00_volume 0 6.856 14.328 33.1335366893279 34.872 2427.944 0
part_00_electrons 0 3.4324799905 7.783738288 17.6294861845862 19.3093905375 441.1374407 0
part_00_mean 0 0.363105079825 0.51463737475 0.60170541369399 0.717429216975 8.596871096 0
part_00_std 0 0.064236985965 0.1210435661 0.209551866773866 0.23328975395 8.010635794 0
part_00_max 0 0.56509415805 0.8888492286 1.35413509828394 1.506440222 44.63356781 0
part_00_max_over_std 0 5.23370953075 7.2410710645 9.766839548402 11.2927055825 173.2519886 0
part_00_skewness 0 0.05595256506 0.11086069425 0.215817126759591 0.23349291195 10.50955383 2
part_00_parts 0 1 1 1.07092783720033 1 28 0
part_00_shape_O3 121.3947368 27057.0207475 97222.576165 1695479.56498225 608579.833125 2628816578 6
part_00_shape_O4 3807.052632 181656262.075 2333791302 10797740453895.3 76345986842.5 4.338385464e+17 6
part_00_shape_O5 33777.02632 337713238000 15383126150000 1.81500729804873e+20 2266284574500000 2.908411654e+25 6
part_00_shape_FL 75.70408004 916394745.875 39080558925 62327442959780432 5624132323500 8.380412043e+21 6
part_00_shape_O3_norm 0.2305739889 0.270932235625 0.38348836015 0.494452362404451 0.6108486294 39.64691261 6
part_00_shape_O4_norm 0.01756274188 0.0217118341525 0.03388987025 0.0618813374712343 0.06955462012 6.010881387 6
part_00_shape_O5_norm 0.0004262883158 0.000513124528 0.0007722045561 0.00199060865767354 0.00176993665425 0.4110453704 6
part_00_shape_FL_norm 1.134335211e-07 0.00063401688275 0.0056627527875 0.0568302783374848 0.0321326354675 189.3506959 6
part_00_shape_I1 479.8371004 1194049.1195 7855760.194 3000624917.82367 135109135.55 163322206500000 6
part_00_shape_I2 56939.7087 219066700525 9063620757500 2.96404467406671e+20 2084935175750000 3.58305756e+25 6
part_00_shape_I3 49989.15888 529484036050 25210998480000 8.69401592072794e+22 9158165266250000 2.665214001e+28 6
part_00_shape_I4 42.46570174 467420883.275 21415867520 35090178451447548 3380179159000 4.526597788e+21 6
part_00_shape_I5 2.451835149 72011194.6475 6438371323 16932002111629766 1430157044750 1.957388285e+21 6
part_00_shape_I6 22342.79801 14397295055 347048438700 1680470065959411968 42027035162500 3.743293967e+23 6
part_00_shape_I1_norm 0.06322810516 0.099123468235 0.23224509785 0.55832827200875 0.597536216825 2760.572581 6
part_00_shape_I2_norm 0.001040183787 0.00195449720925 0.006747190324 0.0911755011626962 0.035455551735 303.9073125 6
part_00_shape_I3_norm 0.0008016258967 0.00313897274 0.02540066147 31.3744237593425 0.198875116775 7617375.322 6
part_00_shape_I4_norm 4.590246527e-08 0.000293604645125 0.0031912351115 0.0387685575170504 0.0198827000175 189.0716741 6
part_00_shape_I5_norm 1.433670721e-10 4.18361131125e-05 0.0010844612885 0.0267274103034399 0.00966937123725 188.8856596 6
part_00_shape_I6_norm 0.004862942323 0.0107157755525 0.043569366905 0.86694327376586 0.198634037575 109414.6959 6
part_00_shape_M000 38 857 1791 4141.7352497742 4359 303493 6
part_00_shape_CI -129.4545845 -0.79430445765 0.0002969493295 0.0461305970679179 0.84061899865 70.04395863 6
part_00_shape_E3_E1 6.638587028e-05 0.0864778723025 0.17003142535 0.24235343864368 0.35560261055 0.9947771112 6
part_00_shape_E2_E1 0.000128514727 0.215891090125 0.3819474389 0.423876545882786 0.614735544825 1 6
part_00_shape_E3_E2 0.01144195139 0.36984490035 0.57076422825 0.552831054820276 0.7423507087 1 6
part_00_shape_sqrt_E1 1.076346776 4.03505970775 5.892465523 8.05604991703898 10.0915915 202.7615055 6
part_00_shape_sqrt_E2 0.738902385 2.597322666 3.518080126 4.44354458691352 5.26993273625 34.51639297 6
part_00_shape_sqrt_E3 0.5959134156 1.9530732195 2.5897241265 2.94632383341524 3.47936533475 20.34264666 6
part_00_density_O3 9.711224684 13005.5724725 47560.76906 801019.914185333 268997.705975 567372596.1 6
part_00_density_O4 24.38308404 41663209.8325 561109355.8 1363855549730.82 14706761645 2.005882204e+16 6
part_00_density_O5 17.32080844 36960799762.5 1803784086500 1746409063047778560 189727098050000 1.807558764e+23 6
part_00_density_FL -3.009896981 172450124.6 8607309656 3734748385523714 1178770349500 4.048898964e+20 6
part_00_density_O3_norm 0.03559376981 0.3846557317 0.6088333939 0.751393069472097 0.96385940315 412.328286 6
part_00_density_O4_norm 0.0004207922565 0.04164163407 0.08846415947 0.147616610196422 0.18082061785 32.92661752 6
part_00_density_O5_norm 1.652895249e-06 0.0012633898925 0.00322639427 0.0078284383686351 0.00782691997625 27.99506456 6
part_00_density_FL_norm -0.03476061339 0.00201224585825 0.018983227155 0.347878948297929 0.12975471975 29271.04832 6
part_00_density_I1 42.2229442 547754.671375 3484281.7855 1051219473.27715 58344659.085 12820833470000 6
part_00_density_I2 363.0952973 45546422817.5 1797947969000 13843497090749585408 3.74152866e+14 1.508584529e+24 6
part_00_density_I3 503.5110024 112113904625 4966128197000 1.00083653298471e+21 1758885410750000 1.642551475e+26 6
part_00_density_I4 -1.005383674 92055091.6875 5189857717.5 2248578330649368 790615926800 2.341519885e+20 6
part_00_density_I5 0.03176528962 19916881.06 2029519085 1257798293952136 411220406000 1.203267165e+20 6
part_00_density_I6 182.7383907 3168079696 73302795715 40942961992870536 8197618476750 5.254844754e+21 6
part_00_density_I1_norm 0.001747813076 0.218069055275 0.5819320415 2.44445273171427 1.538936734 298590.9488 6
part_00_density_I2_norm 8.053167968e-07 0.00884582893425 0.046127570835 0.749308558824666 0.242191741325 7616.408967 6
part_00_density_I3_norm 6.251427124e-07 0.015648092145 0.1517720267 179056.280189339 1.31012996425 89117182130 6
part_00_density_I4_norm -0.01161094662 0.0010091733 0.011509753725 0.279274932530713 0.0865742033125 29231.84652 6
part_00_density_I5_norm 1.637856779e-10 0.0001977232373 0.0048093909295 0.233538922006994 0.049697683875 29205.71198 6
part_00_density_I6_norm 2.090698844e-05 0.034241724925 0.16769547215 296.843746955821 0.7961212752 123080053.3 6
part_00_density_M000 1.864285111 429.0678462 972.9981363 2203.7087392988 2413.69359325 55142.18009 6
part_00_density_CI -155.701412 -0.858521445575 0.00019182554265 0.0475445073795394 0.903993823875 89.96053361 6
part_00_density_E3_E1 6.604160143e-05 0.08309210098 0.16864460925 0.24508064974345 0.36542509365 0.9958993203 6
part_00_density_E2_E1 0.0001276943492 0.211137407875 0.3819973684 0.423951283523217 0.619479032825 0.9999998643 6
part_00_density_E3_E2 0.01305281121 0.3687294446 0.57491832355 0.554827419624812 0.74782409465 0.9999999613 6
part_00_density_sqrt_E1 1.072152367 3.7699128855 5.573238223 7.73700324469222 9.76148380475 202.4822866 6
part_00_density_sqrt_E2 0.7382289477 2.45726224425 3.2819451615 4.21820399021366 4.98578883075 32.97918301 6
part_00_density_sqrt_E3 0.5954518305 1.86961842875 2.4330287475 2.78243633755072 3.24031132325 19.37849776 6
part_00_shape_Z_7_3 6.30312003 15.6230944375 26.71808221 41.1237462309464 53.5526852575 558.7070258 6
part_00_shape_Z_0_0 3.011948166 14.30362469 20.6777599 26.2662245907247 32.25886848 269.172095 6
part_00_shape_Z_7_0 0.6818404009 6.50426107825 10.213001845 17.4144565952786 22.1540931025 366.9916795 6
part_00_shape_Z_7_1 3.661825436 9.957970248 17.669219445 28.2555942748209 37.0077526775 446.1359298 6
part_00_shape_Z_3_0 0.571422094 5.99214178525 10.70816582 15.1108089527818 19.63898586 208.1280084 6
part_00_shape_Z_5_2 4.580256005 14.715472825 24.82553103 35.0866284669985 45.298087505 455.101189 6
part_00_shape_Z_6_1 1.807757938 12.040449195 20.946944805 31.812024920542 42.408123735 476.2128169 6
part_00_shape_Z_3_1 2.505837245 11.3511645375 18.144064605 24.4783464264835 30.90780641 297.2757961 6
part_00_shape_Z_6_0 0.02436425529 5.50200848575 9.9224029715 14.8506736545214 19.27195294 299.0132519 6
part_00_shape_Z_2_1 2.429600076 19.40950579 28.78839488 38.4147364562564 48.2438118075 420.8093352 6
part_00_shape_Z_6_3 4.113508963 18.75763798 31.270307195 46.6883901055614 61.35824783 608.4310162 6
part_00_shape_Z_2_0 1.049642044 14.37872129 21.86555755 28.2164785088653 35.548141675 326.5258558 6
part_00_shape_Z_6_2 2.941402487 16.4335561575 28.025620615 42.1698856754525 55.767869235 562.2021526 6
part_00_shape_Z_5_0 0.7928716828 5.63076741125 12.25827021 18.341775594047 24.4667285 315.573314 6
part_00_shape_Z_5_1 3.463939546 11.5003167725 20.557661095 29.0088948845917 37.8237976825 407.4940969 6
part_00_shape_Z_4_2 3.536957069 19.2395184775 31.432084135 43.9385813428476 57.058548525 534.4743816 6
part_00_shape_Z_1_0 0.7373045028 1.26192610125 1.404309371 1.42541623162108 1.5670765735 2.525211314 6
part_00_shape_Z_4_1 1.94972829 16.0527778625 27.07137287 37.8083117458604 49.7330362975 465.6008098 6
part_00_shape_Z_7_2 5.741843786 13.277177295 23.42865461 36.5547716038074 47.899136875 530.3215832 6
part_00_shape_Z_4_0 0.02954763925 8.232657805 14.91412993 20.5455788797275 27.39525068 313.0934259 6
part_00_density_Z_7_3 2.894867781 10.686300995 19.57205548 30.4553825486114 39.50216056 211.1186257 6
part_00_density_Z_0_0 0.6671321355 10.1208894325 15.24093811 19.1328271408767 24.00472661 114.7354601 6
part_00_density_Z_7_0 0.9849014403 5.983010466 8.579471565 14.9279220846135 19.0133855125 126.9187798 6
part_00_density_Z_7_1 2.877502984 7.48929576825 14.0335003 22.4186491071828 29.3099305175 159.9190948 6
part_00_density_Z_3_0 0.4221085286 4.43414719825 7.809777715 11.3500855817079 14.557800735 88.53859908 6
part_00_density_Z_5_2 2.150798646 10.02689568 17.84693627 25.6458810018479 33.302145775 182.1829673 6
part_00_density_Z_6_1 0.4343871441 7.65719229 17.233605405 24.8344567149988 33.8130627575 196.0674613 6
part_00_density_Z_3_1 1.444641718 7.57215946425 12.517145155 17.3706916024529 22.06254339 120.8635572 6
part_00_density_Z_6_0 0.007071927991 3.59944586175 8.1019986195 12.5949888289052 17.26946858 122.4933814 6
part_00_density_Z_2_1 0.7737221038 14.2676430725 21.574873275 28.1465605955064 34.981755755 176.3804765 6
part_00_density_Z_6_3 0.5448886683 12.1694018375 23.670134555 34.4019352482212 45.4517455925 282.8048412 6
part_00_density_Z_2_0 0.3606986122 10.98726405 17.057697155 21.6710817580159 27.79138064 135.276743 6
part_00_density_Z_6_2 0.4772227986 10.7704268525 21.81239755 31.6558979266011 42.2018417175 263.894204 6
part_00_density_Z_5_0 0.8740978443 5.13349933925 9.800981217 14.9658293492077 19.5972352825 118.2291655 6
part_00_density_Z_5_1 2.141748592 8.24944651975 15.30460767 21.9599126016601 28.8064361275 167.0803952 6
part_00_density_Z_4_2 0.5863015808 14.2823776825 23.620486935 32.412366435862 41.7400361 236.6704082 6
part_00_density_Z_1_0 0.676804413 1.25011103 1.393010576 1.41602373112303 1.561421691 2.524396793 6
part_00_density_Z_4_1 0.4739294732 12.58629058 21.055664985 28.6639689364339 37.27805028 204.5133587 6
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part_01_shape_O3_norm 0.2273854245 0.2600788512 0.36671078095 0.534332827070869 0.67272941955 43.7516017 5440
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part_02_shape_segments_count 0 2 9 238.344472891619 64 45564 0
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part_02_shape_FL -61.15935744 15757367.46 3460179126.5 20792723621479068 1283444917250 3.330358279e+21 39702
part_02_shape_O3_norm 0.2269145962 0.252823889925 0.33986987515 0.576596796112792 0.72544657455 68.88374187 39702
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part_02_shape_FL_norm -1.917847392e-05 0.000223390213975 0.003036618026 0.356666363091967 0.0604095641425 3374.84244 39702
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part_02_shape_I4_norm -6.478741585e-06 9.785099142e-05 0.0016810030595 0.320976282269867 0.0407703933125 3367.003644 39702
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part_02_shape_I6_norm 0.004609744519 0.007787616906 0.029931113065 3.02337420356417 0.35699184865 575558.1108 39702
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part_02_shape_CI -153.7476975 -0.465816351425 8.7582609795e-05 0.0312865058382261 0.49248775785 147.0380863 39702
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part_02_density_O3 9.46406785 4555.53294975 25477.65995 594880.09378333 164893.795675 422873659.4 39702
part_02_density_O4 26.47290094 4808538.35325 154607381.45 768277832931.513 5406225111 1.060964832e+16 39702
part_02_density_O5 19.57740725 1413065261.75 256873803000 675171599751762816 42366473562500 6.745875771e+22 39702
part_02_density_FL -23.32580548 5078585.41125 1157646567.5 2099456805735417 446837849375 2.126358836e+20 39702
part_02_density_O3_norm 0.03293952489 0.320998654975 0.51047334995 0.777368432201909 0.965283057125 382.9768645 39702
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part_02_density_O5_norm 1.320574892e-06 0.00083098379735 0.002213842025 0.00935395532604198 0.006431268816 113.0485047 39702
part_02_density_FL_norm -0.004686326327 0.0005567944075 0.0066044615425 2.32177617891657 0.1493438097 197912.7855 39702
part_02_density_I1 26.90263097 111870.2857 1350646.141 770781966.076257 31631680.045 9365255920000 39702
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part_02_density_I3 162.2540673 4171797142.5 674704013750 5.5292879315094e+20 554792820050000 8.766542159e+25 39702
part_02_density_I4 -5.770646085 2443559.02875 666766726.3 1342962137663308 319285565900 1.31442451e+20 39702
part_02_density_I5 0.0002899668474 343057.974875 190859719.85 838632358922868 178789474625 7.731349589e+19 39702
part_02_density_I6 88.32222845 226539462.85 15542664580 23518571592212004 2767427247000 2.750679082e+21 39702
part_02_density_I1_norm 0.001492929285 0.1432702702 0.3926676432 3.00463023855793 1.61836514375 258303.8672 39702
part_02_density_I2_norm 5.929662497e-07 0.00411563307825 0.022854090795 11.5034934619185 0.227504833525 2154055.586 39702
part_02_density_I3_norm 4.480855128e-07 0.006156361564 0.063868690145 149071.179621009 1.54129865525 66708791400 39702
part_02_density_I4_norm -0.001808171149 0.0002545523456 0.0038807222625 2.38647363837757 0.10799313355 264833.3131 39702
part_02_density_I5_norm 1.157187674e-10 2.895409806e-05 0.0015236418635 2.42960527805216 0.0665502713075 309446.9982 39702
part_02_density_I6_norm 1.642012403e-05 0.0180519646 0.09089457529 254.496948974585 0.8676927075 98912031.52 39702
part_02_density_M000 2.538354646 234.029745475 692.44037595 1739.47210148389 1966.34057925 43898.33204 39702
part_02_density_CI -166.928922 -0.488644906875 6.4344343615e-05 0.0297757557168502 0.510791552175 167.5373289 39702
part_02_density_E3_E1 3.077645341e-05 0.0738855604825 0.1995912299 0.270382630574708 0.434014719525 0.9964265156 39702
part_02_density_E2_E1 4.898493277e-05 0.202735579175 0.41535099 0.439309947009086 0.660192483975 0.9999999682 39702
part_02_density_E3_E2 0.009932988958 0.392107933975 0.61837762295 0.577576713405616 0.7772478897 0.9999999766 39702
part_02_density_sqrt_E1 0.9318626049 2.8179456865 4.4102065865 6.89287411221691 9.07444980675 201.7050834 39702
part_02_density_sqrt_E2 0.5635506026 1.8984330805 2.7472572575 3.64770540560666 4.351791953 32.35449294 39702
part_02_density_sqrt_E3 0.4014297725 1.4820386485 2.093738484 2.39116401624088 2.8762564935 17.84455462 39702
part_02_shape_Z_7_3 5.83960079 10.95182318 18.58391625 32.7766026873652 42.7081337025 416.5654831 39702
part_02_shape_Z_0_0 2.763953196 9.723067222 15.87018265 20.147430614394 25.32262359 220.7202022 39702
part_02_shape_Z_7_0 0.9095853601 6.78265832475 8.474385616 15.2669465899787 18.23870205 228.8372883 39702
part_02_shape_Z_7_1 3.760529496 8.452370902 12.23535068 23.1681397127822 29.80664404 319.7387226 39702
part_02_shape_Z_3_0 0.4922365492 4.4493366335 7.6246062965 12.4464497816764 16.344487415 195.1590497 39702
part_02_shape_Z_5_2 3.978093159 9.084246169 17.43752889 27.4420867306156 35.9858526475 344.7866219 39702
part_02_shape_Z_6_1 0.971167048 7.2828897715 14.290491325 24.5333529910363 33.0763657675 340.5182007 39702
part_02_shape_Z_3_1 2.615481061 7.162718439 13.53123637 19.3983181791035 24.9850614725 261.961261 39702
part_02_shape_Z_6_0 0.002431445993 3.44720971775 6.995242045 11.9289881262018 15.3220231875 204.6875772 39702
part_02_shape_Z_2_1 1.587596451 12.58147584 21.060789165 29.1206179674716 37.3633818875 315.9119291 39702
part_02_shape_Z_6_3 3.177852956 11.16967189 21.823906075 36.0692148597777 48.48289561 495.4178011 39702
part_02_shape_Z_2_0 0.05221444873 8.8764735855 15.58819009 21.0831377924912 27.313042865 264.7737438 39702
part_02_shape_Z_6_2 2.169626771 9.60316095675 19.086345765 32.2652896361917 43.5397600275 461.0860046 39702
part_02_shape_Z_5_0 0.7615551244 5.5291010585 7.9410453025 15.315489520728 20.0348455575 241.832509 39702
part_02_shape_Z_5_1 2.705489715 7.41826726525 13.95902084 22.6272674895301 29.7633400925 300.3947766 39702
part_02_shape_Z_4_2 2.174361229 11.415190415 21.63106506 33.2315383129167 44.39495124 412.1893426 39702
part_02_shape_Z_1_0 0.6729881274 1.33626038675 1.5875655115 1.65203204494229 1.8719790345 5.053228749 39702
part_02_shape_Z_4_1 0.8847612903 9.0189049465 18.005069035 28.1730608540004 38.10938988 355.2037823 39702
part_02_shape_Z_7_2 4.534117032 9.758163834 15.86383032 29.0252741518712 37.728873865 382.3021123 39702
part_02_shape_Z_4_0 0.009469098667 4.64735286925 9.534040697 15.4366974336642 20.920627515 247.7431767 39702
part_02_density_Z_7_3 3.205354241 9.372090008 14.5484575 26.9787046973951 34.8969087975 200.1822739 39702
part_02_density_Z_0_0 0.7784520113 7.47465626175 12.85721443 16.3660078715098 21.6663156675 102.3716504 39702
part_02_density_Z_7_0 0.952241736 6.51356552875 8.066543796 14.1530749066335 16.767902805 122.9814966 39702
part_02_density_Z_7_1 1.985287665 7.688617466 10.357224035 20.184689267479 25.6340453675 151.618603 39702
part_02_density_Z_3_0 0.5339320117 4.14633999325 6.2251214255 10.4396666470794 13.3790933725 83.37841647 39702
part_02_density_Z_5_2 2.333199775 7.7132597825 13.68352834 22.4233201636486 29.5256174625 178.4799195 39702
part_02_density_Z_6_1 0.4645438648 5.08653844275 11.412295125 20.6536988439468 29.26476223 185.8141834 39702
part_02_density_Z_3_1 1.9646589 5.83998322925 10.31664064 15.4909861945341 20.03386739 113.8338572 39702
part_02_density_Z_6_0 0.0005344082229 2.44753902225 5.201348063 10.7199911148064 14.706057065 115.1505833 39702
part_02_density_Z_2_1 0.7793738898 10.23846919 17.66268559 23.7705085344482 30.72985265 165.2802441 39702
part_02_density_Z_6_3 0.9761576627 7.8368919375 17.064881265 29.0878916812011 40.09359629 257.0873277 39702
part_02_density_Z_2_0 0.02936858271 7.50111499175 13.563926415 18.0357062103476 24.3790405625 120.5566076 39702
part_02_density_Z_6_2 0.7662380856 6.6980886665 15.24479204 26.4059686276437 36.68089811 242.5491618 39702
part_02_density_Z_5_0 0.6352722861 5.37321612575 7.455046631 13.6707422595879 17.447302955 111.3185305 39702
part_02_density_Z_5_1 1.68343546 6.70053440925 11.31865804 19.0947615319076 25.1615600125 162.4163936 39702
part_02_density_Z_4_2 0.7775913047 8.53880109975 18.077851205 26.9512001448052 36.554214565 214.2124261 39702
part_02_density_Z_1_0 0.6087433634 1.32398143025 1.5804985995 1.64451789979272 1.8694510785 5.050802593 39702
part_02_density_Z_4_1 0.3994020304 6.92388709025 15.6675129 23.3898528814388 32.113628065 187.5631296 39702
part_02_density_Z_7_2 2.609323469 8.5956354925 12.778000365 24.4172710099089 31.4669965975 188.3994704 39702
part_02_density_Z_4_0 0.005330786982 3.361982422 8.923390504 13.7930174215912 19.5086235125 119.3436982 39702
fo_col 575726 character character 575726 character character 575726
fc_col 575726 character character 575726 character character 575726
weight_col logical 575726 logical 575726 logical 575726 logical
grid_space 0.2 0.2 0.2 0.2 0.2 0.2 0.2
solvent_radius 1.9 1.9 1.9 1.9 1.9 1.9 1.9
solvent_opening_radius 1.4 1.4 1.4 1.4 1.4 1.4 1.4
resolution_max_limit 1 1 1 1 1 1 1
resolution 0.4800812304 1.79998827 2.076049328 2.15048560488871 2.482087612 8.999694824 0.4800812304
FoFc_mean -1.942057963e-07 -4.618861196e-11 7.822532769e-13 4.25100650827451e-11 4.964862549e-11 3.621388771e-07 -1.942057963e-07
FoFc_std 0.001250090112 0.09013658464 0.1223734106 0.128956289622333 0.1591430283 0.9418859565 0.001250090112
FoFc_square_std 1.562725288e-06 0.00812460389 0.01497525163 0.0195485813333313 0.02532650344 0.8871491551 1.562725288e-06
FoFc_min -10.821105 -0.848829031 -0.6640108824 -0.700363778077503 -0.499686718 -0.01075177453 -10.821105
FoFc_max 0.007184891496 1.141174555 1.847463131 2.60529588208993 3.082387924 45.26153183 0.007184891496
part_step_FoFc_std_min 2.8 2.8 2.8 2.8 2.8 2.8 2.8
part_step_FoFc_std_max 4.05 4.05 4.05 4.05 4.05 4.05 4.05
part_step_FoFc_std_step 0.5 0.5 0.5 0.5 0.5 0.5 0.5

Ograniczanie zbioru

Kod ograniczający liczbę klas (res_name) do 50 najpopularniejszych wartości.

most_popular <- all_summary %>% group_by(res_name) %>% summarise(count=n()) %>% arrange(desc(count)) %>% head(50)
all_summary %<>% filter(res_name %in% most_popular$res_name)

Korelacja zmiennych

Sekcja sprawdzająca korelacje między zmiennymi; sekcja ta powinna zawierać jakąś formę graficznej prezentacji korelacji.

atom_non_h_count

ggplot(all_summary, aes(x=local_res_atom_non_h_count, y=dict_atom_non_h_count)) + geom_point() + ggtitle("local_res_atom_non_h_count vs dict_atom_non_h_count") + geom_smooth(method=lm, se=FALSE) + scale_x_continuous(name = "local_res_atom_non_h_count") + scale_y_continuous(name = "dict_atom_non_h_count") + theme(plot.title = element_text(hjust = 0.5), panel.background = element_blank(), axis.line = element_line(color="black"), axis.line.x = element_line(color="black")) + theme_bw()

atom_non_h_electron_sum

ggplot(all_summary, aes(x=local_res_atom_non_h_electron_sum, y=dict_atom_non_h_electron_sum )) + geom_point() + ggtitle("local_res_atom_non_h_electron_sum vs dict_atom_non_h_electron_sum ") + geom_smooth(method=lm, se=FALSE) + scale_x_continuous(name = "local_res_atom_non_h_electron_sum") + scale_y_continuous(name = "dict_atom_non_h_electron_sum ") + theme(plot.title = element_text(hjust = 0.5), panel.background = element_blank(), axis.line = element_line(color="black"), axis.line.x = element_line(color="black")) + theme_bw()

atom_C_count

ggplot(all_summary, aes(x=local_res_atom_C_count, y=dict_atom_C_count )) + geom_point() + ggtitle("local_res_atom_C_count vs dict_atom_C_count ") + geom_smooth(method=lm, se=FALSE) + scale_x_continuous(name = "local_res_atom_C_count") + scale_y_continuous(name = "dict_atom_C_count ") + theme(plot.title = element_text(hjust = 0.5), panel.background = element_blank(), axis.line = element_line(color="black"), axis.line.x = element_line(color="black")) + theme_bw()

atom_N_count

ggplot(all_summary, aes(x=local_res_atom_N_count, y=dict_atom_N_count )) + geom_point() + ggtitle("local_res_atom_N_count vs dict_atom_N_count ") + geom_smooth(method=lm, se=FALSE) + scale_x_continuous(name = "local_res_atom_N_count") + scale_y_continuous(name = "dict_atom_N_count ") + theme(plot.title = element_text(hjust = 0.5), panel.background = element_blank(), axis.line = element_line(color="black"), axis.line.x = element_line(color="black")) + theme_bw()

atom_O_count

ggplot(all_summary, aes(x=local_res_atom_O_count, y=dict_atom_O_count)) + geom_point() + ggtitle("local_res_atom_O_count vs dict_atom_O_count") + geom_smooth(method=lm, se=FALSE) + scale_x_continuous(name = "local_res_atom_O_count") + scale_y_continuous(name = "dict_atom_O_count") + theme(plot.title = element_text(hjust = 0.5), panel.background = element_blank(), axis.line = element_line(color="black"), axis.line.x = element_line(color="black")) + theme_bw()

atom_S_count

ggplot(all_summary, aes(x=local_res_atom_S_count, y=dict_atom_S_count)) + geom_point() + ggtitle("local_res_atom_S_count vs dict_atom_S_count") + geom_smooth(method=lm, se=FALSE) + scale_x_continuous(name = "local_res_atom_S_count") + scale_y_continuous(name = "dict_atom_S_count") + theme(plot.title = element_text(hjust = 0.5), panel.background = element_blank(), axis.line = element_line(color="black"), axis.line.x = element_line(color="black")) + theme_bw()

Liczba przykładów

Określenie ile przykładów ma każda z klas (res_name).

kable(most_popular %>% select(res_name, count)) %>%
  kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = FALSE)
res_name count
SO4 56572
GOL 40606
EDO 30825
NAG 26360
CL 23223
CA 21038
ZN 19826
MG 14779
HEM 11192
PO4 11090
ACT 8096
DMS 6633
IOD 6317
PEG 4987
CLA 4784
K 4706
FAD 4555
NAD 4501
MN 4215
ADP 3819
MLY 3509
NAP 3505
CD 3242
MPD 3221
FMT 2918
MAN 2841
PG4 2768
MES 2697
CU 2353
ATP 2296
COA 2183
1PE 2136
BR 2127
NDP 2106
FMN 2084
EPE 1933
HEC 1917
PGE 1905
TRS 1656
SF4 1647
NI 1637
ACY 1609
FE 1602
NO3 1596
PLP 1594
GDP 1589
SAH 1587
FE2 1560
SEP 1491
CIT 1464

Rozkład liczby atomów i elektronów

Wykresy rozkładów liczby atomów (local_res_atom_non_h_count) i elektronów (local_res_atom_non_h_electron_sum).

Rozkład liczby atomów

ggplotly(ggplot(data=all_summary, aes(all_summary$local_res_atom_non_h_count)) + geom_histogram(binwidth = 1, col = "black", fill="blue", alpha = .2) + ggtitle("Rozkład liczby atomów") + scale_x_continuous("Liczba atomów"))

Rozkład liczby elektronów

ggplotly(ggplot(data=all_summary, aes(all_summary$local_res_atom_non_h_electron_sum)) + geom_histogram(binwidth = 1, col = "black", fill="blue", alpha = .2) + ggtitle("Rozkład liczby elektronów") + scale_x_continuous("Liczba elektronów"))

Niezgodność liczby atomów i elektronów

Tabela pokazująca 10 klas z największą niezgodnością liczby atomów (local_res_atom_non_h_count vs dict_atom_non_h_count) i tabelę pokazującą 10 klas z największą niezgodnością liczby elektronów (local_res_atom_non_h_electron_sum vs dict_atom_non_h_electron_sum;)

Niezgodność liczby atomów

kable(all_summary %>% filter(!is.na(res_name)) %>% group_by(res_name) %>% summarise(mean_incompatibility = mean(abs(local_res_atom_non_h_count - dict_atom_non_h_count), na.rm = TRUE)) %>% arrange(desc(mean_incompatibility)) %>% head(10)) %>%
  kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = FALSE)
res_name mean_incompatibility
CLA 5.2451923
1PE 2.6633895
COA 1.8346312
MLY 1.3265888
NAP 1.2833096
PG4 1.0440751
SEP 1.0087190
NDP 0.9881292
NAG 0.9801214
MAN 0.8944034

Niezgodność liczby elektronów

kable(all_summary %>% filter(!is.na(res_name)) %>% group_by(res_name) %>%  summarise(mean_incompatibility = mean(abs(local_res_atom_non_h_electron_sum - dict_atom_non_h_electron_sum), na.rm = TRUE)) %>% arrange(desc(mean_incompatibility)) %>% head(10)) %>%
  kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = FALSE)
res_name mean_incompatibility
CLA 31.846990
1PE 18.161985
COA 13.783326
MLY 9.976062
NAP 8.630242
SEP 8.126090
NAG 7.838695
MAN 7.155227
PG4 7.059971
PLP 6.874530

Rozkład wartości zmiennych part_01

Sekcja pokazująca rozkład wartości wszystkich kolumn zaczynających się od part_01 z zaznaczeniem (graficznym i liczbowym) średniej wartości.

for (name in names(all_summary %>% select(starts_with("part_01"))) %>% tail(1)) {
print(ggplot(data=all_summary, aes(all_summary[[name]])) + geom_histogram(binwidth = 1, col = "black", fill="blue", alpha = .2) + geom_vline(aes(xintercept = mean(all_summary[[name]], na.rm = T)), color="red", linetype="dotted", size=1) + scale_x_continuous(name = name,breaks = mean(all_summary[[name]], na.rm = T)))
}

Interaktywny wykres lub animację.

Interaktywne wykresy stworzono dla rozkładów wartości atomów i elektronów.

Regresja

Sekcja sprawdzająca czy na podstawie wartości innych kolumn można przewidzieć liczbę elektronów i atomów oraz z jaką dokładnością można dokonać takiej predykcji; trafność regresji powinna zostać oszacowana na podstawie miar R^2 i RMSE;

gy <- c("local_volume", "local_electrons", "local_mean", "local_std", "local_min", "local_max", "local_skewness", "resolution")
all_summary %<>% head(50000)

Liczba atomów

all_summary_atoms <- all_summary %>% select(starts_with("part_0"), local_res_atom_non_h_count, starts_with("FoFc_"), gy) %>% na.omit() 

idx <- createDataPartition(all_summary_atoms$local_res_atom_non_h_count, p=0.7, list=FALSE)
trainingData <- data.frame(all_summary_atoms[idx,])
testData <- data.frame(all_summary_atoms[-idx,])

ctrl <- trainControl(
    # powtórzona ocena krzyżowa
    method = "repeatedcv",
    # liczba podziałów
    number = 2,
    # liczba powtórzeń
    repeats = 5)

train(local_res_atom_non_h_count ~ .,
             data = trainingData,
             method = "lm",
             trControl = ctrl)
## Linear Regression 
## 
## 32867 samples
##   331 predictor
## 
## No pre-processing
## Resampling: Cross-Validated (2 fold, repeated 5 times) 
## Summary of sample sizes: 16434, 16433, 16434, 16433, 16433, 16434, ... 
## Resampling results:
## 
##   RMSE      Rsquared   MAE     
##   47.03144  0.2036114  5.225487
## 
## Tuning parameter 'intercept' was held constant at a value of TRUE

Liczba elektronów

all_summary_electrons <- all_summary %>% select(starts_with("part_0"), local_res_atom_non_h_electron_sum, starts_with("FoFc_"), gy) %>% na.omit()

idx <- createDataPartition(all_summary_electrons$local_res_atom_non_h_electron_sum, p=0.7, list=FALSE)
trainingData <- data.frame(all_summary_electrons[idx,])
testData <- data.frame(all_summary_electrons[-idx,])

ctrl <- trainControl(
    # powtórzona ocena krzyżowa
    method = "repeatedcv",
    # liczba podziałów
    number = 2,
    # liczba powtórzeń
    repeats = 5)

train(local_res_atom_non_h_electron_sum ~ .,
             data = trainingData,
             method = "lm",
             trControl = ctrl)
## Linear Regression 
## 
## 32868 samples
##   331 predictor
## 
## No pre-processing
## Resampling: Cross-Validated (2 fold, repeated 5 times) 
## Summary of sample sizes: 16433, 16435, 16433, 16435, 16433, 16435, ... 
## Resampling results:
## 
##   RMSE     Rsquared   MAE     
##   114.627  0.2928972  33.59331
## 
## Tuning parameter 'intercept' was held constant at a value of TRUE

Klasyfikacja

Sekcja próbująca stworzyć klasyfikator przewidujący wartość atrybutu res_name (w tej sekcji należy wykorzystać wiedzę z pozostałych punktów oraz wykonać dodatkowe czynności, które mogą poprawić trafność klasyfikacji); trafność klasyfikacji powinna zostać oszacowana na danych inne niż uczące za pomocą mechanizmu (stratyfikowanej!) oceny krzyżowej lub (stratyfikowanego!) zbioru testowego.

all_summary %<>% select(starts_with("part_0"), res_name, starts_with("FoFc_"), gy) %>% na.omit()
inTraining <- 
    createDataPartition(
        # atrybut do stratyfikacji
        y = all_summary$res_name,
        # procent w zbiorze uczącym
        p = .75,
        # chcemy indeksy a nie listę
        list = FALSE)

training <- all_summary[ inTraining,]
testing  <- all_summary[-inTraining,]

ctrl <- trainControl(
    # powtórzona ocena krzyżowa
    method = "repeatedcv",
    # liczba podziałów
    number = 2,
    # liczba powtórzeń
    repeats = 5)

fit <- train(res_name ~ .,
             data = training,
             method = "rf",
             trControl = ctrl,
             ntree = 10)

fit
## Random Forest 
## 
## 35232 samples
##   331 predictor
##    50 classes: '1PE', 'ACT', 'ACY', 'ADP', 'ATP', 'BR', 'CA', 'CD', 'CIT', 'CL', 'CLA', 'COA', 'CU', 'DMS', 'EDO', 'EPE', 'FAD', 'FE', 'FE2', 'FMN', 'FMT', 'GDP', 'GOL', 'HEC', 'HEM', 'IOD', 'K', 'MAN', 'MES', 'MG', 'MLY', 'MN', 'MPD', 'NAD', 'NAG', 'NAP', 'NDP', 'NI', 'NO3', 'PEG', 'PG4', 'PGE', 'PLP', 'PO4', 'SAH', 'SEP', 'SF4', 'SO4', 'TRS', 'ZN' 
## 
## No pre-processing
## Resampling: Cross-Validated (2 fold, repeated 5 times) 
## Summary of sample sizes: 17617, 17615, 17617, 17615, 17614, 17618, ... 
## Resampling results across tuning parameters:
## 
##   mtry  Accuracy   Kappa    
##     2   0.3831461  0.3273827
##   166   0.4189545  0.3673255
##   331   0.4185630  0.3671520
## 
## Accuracy was used to select the optimal model using the largest value.
## The final value used for the model was mtry = 166.
rf_res_names <- predict(fit, newdata = testing)
confusionMatrix(table(data = rf_res_names, testing$res_name))
## Confusion Matrix and Statistics
## 
##      
## data   1PE  ACT  ACY  ADP  ATP   BR   CA   CD  CIT   CL  CLA  COA   CU
##   1PE   11    0    1    0    0    0    0    0    1    0    0    0    0
##   ACT    1   28    5    0    0    1    5    3    1    6    0    0    1
##   ACY    0    0    2    0    0    0    0    0    1    3    0    0    0
##   ADP    0    0    0   31   10    0    1    0    0    0    0    0    0
##   ATP    0    0    0    8   21    0    0    1    1    0    0    0    0
##   BR     0    0    0    0    0   11    0    0    0    6    0    0    0
##   CA     1    3    2    0    0    7  328   11    0   40    0    2   11
##   CD     0    0    0    0    0    3    1   23    0    1    0    0    2
##   CIT    0    0    0    1    1    0    0    0    5    0    0    0    0
##   CL     3   13    7    2    0   21   67    6    2  424    0    4    3
##   CLA    0    0    0    0    0    0    0    0    0    0   21    0    0
##   COA    0    0    0    0    1    0    0    0    0    0    0    3    0
##   CU     0    1    0    0    0    0    3    2    0    2    0    0   10
##   DMS    0    7    0    0    0    1    5    0    0    9    0    1    0
##   EDO   19   52   11    2    3    9   23    1    3   51    0    9    0
##   EPE    1    1    0    0    0    0    1    0    0    1    0    0    0
##   FAD    0    0    0    4    2    0    0    0    0    0    0    1    0
##   FE     0    0    0    0    0    0    0    2    0    3    0    0    0
##   FE2    0    0    0    0    0    0    0    0    0    0    0    0    0
##   FMN    0    0    0    2    0    0    0    0    0    1    0    0    0
##   FMT    0    4    0    0    0    0    0    0    0    0    0    0    0
##   GDP    0    1    0    6    2    0    0    0    0    0    0    0    0
##   GOL   23   41   12    5    4    4   38    3   15   57    0    7    0
##   HEC    0    0    0    0    0    0    0    0    0    0    0    0    0
##   HEM    0    5    0    3    0    0    0    0    1    2    1    1    1
##   IOD    0    0    1    0    0    7    7    7    0    5    0    0    3
##   K      0    1    0    0    0    1    5    1    0    7    0    0    0
##   MAN    1    1    1    0    0    0    1    0    0    0    1    3    0
##   MES    1    0    0    0    0    0    1    0    0    1    0    0    0
##   MG     0    1    2    1    0    0   30    2    0   15    0    0    3
##   MLY    0    1    0    0    0    0    1    0    0    1    0    0    0
##   MN     0    2    1    0    0    0    7    3    0    0    0    1    0
##   MPD    0    1    0    0    0    0    1    0    1    0    0    0    0
##   NAD    0    0    0    3    3    0    1    0    0    1    0    2    0
##   NAG    8    7    2   15   12    1   15    0    9   11    6   14    0
##   NAP    0    0    0    1    0    0    0    0    0    0    0    1    0
##   NDP    0    0    0    1    1    0    0    0    0    0    0    1    0
##   NI     0    0    0    0    0    0    1    0    0    0    0    0    0
##   NO3    0    0    0    0    0    0    0    0    0    1    0    0    0
##   PEG    0    0    1    0    0    0    0    0    1    4    0    2    0
##   PG4    0    0    0    0    0    0    0    0    2    1    0    0    0
##   PGE    0    0    0    0    0    0    0    0    0    1    0    0    0
##   PLP    0    0    0    0    0    0    1    0    0    0    0    1    0
##   PO4    0    4    0    0    0    1    4    0    2    5    0    0    0
##   SAH    0    0    0    5    4    0    1    0    0    0    0    1    0
##   SEP    0    0    0    2    2    0    1    0    0    0    0    0    0
##   SF4    0    1    0    2    0    0    0    0    0    0    0    0    0
##   SO4    4   37   25    7    4   15  109   12    5  126    1   15   10
##   TRS    0    0    0    1    0    0    0    0    0    0    0    0    0
##   ZN     0    9    1    0    0    2   35   24    3    8    0    1   29
##      
## data   DMS  EDO  EPE  FAD   FE  FE2  FMN  FMT  GDP  GOL  HEC  HEM  IOD
##   1PE    1    0    0    0    0    0    0    1    1    4    0    2    0
##   ACT    2    9    1    1    0    1    0    1    0   15    0    3    3
##   ACY    1    1    0    0    0    0    0    1    0    1    0    1    0
##   ADP    0    0    0    0    0    0    2    0   11    3    0    0    0
##   ATP    0    1    0    0    0    0    0    0    1    2    0    0    0
##   BR     1    0    0    0    0    0    0    1    0    0    0    0    2
##   CA     3    7    4    0    3    6    2    0    0   12    1    6   19
##   CD     0    0    0    0    1    0    0    0    1    1    0    0    6
##   CIT    0    0    0    0    0    0    0    0    0    1    0    0    0
##   CL    14   44    3    3    1    1    0    6    1   46    1    4   29
##   CLA    0    0    0    0    0    0    0    0    0    1    0    0    0
##   COA    1    0    0    0    0    0    1    0    0    0    0    1    1
##   CU     0    0    0    0    0    0    0    0    0    0    0    1    2
##   DMS   89   12    0    0    0    0    0    1    0    4    0    1    1
##   EDO   21  465    1    6    3    0    3   23    2  331    4   26    9
##   EPE    0    1   13    0    0    0    0    1    0    1    0    0    0
##   FAD    0    1    0   96    0    0    1    0    1    1    0    3    0
##   FE     0    0    0    0    9    0    0    0    0    0    0    0    0
##   FE2    1    0    0    0    1    4    0    0    0    0    0    0    0
##   FMN    0    0    1    1    0    0   34    0    0    0    0    1    0
##   FMT    1    3    0    0    0    0    0    5    0    5    0    2    0
##   GDP    0    0    0    2    0    0    1    0   19    0    0    0    0
##   GOL   22  284    7    9    1    0    1    8    4  523    5   29    9
##   HEC    0    0    0    0    0    0    0    0    0    0    7    6    0
##   HEM    1    4    0    0    0    0    0    2    0    8   14  219    1
##   IOD    1    1    0    0    0    0    0    1    0    3    0    0   77
##   K      1    0    1    0    0    0    0    1    0    3    0    0    3
##   MAN    0    0    0    0    1    0    0    0    0    4    0    1    0
##   MES    0    1    3    0    1    0    0    0    0    3    0    2    0
##   MG     0   14    0    0    4    0    0    0    0   27    0    2    2
##   MLY    0    0    0    0    0    0    0    0    0    1    0    0    0
##   MN     0    1    0    0    2    4    1    0    1    0    0    0    1
##   MPD    1    3    0    0    0    0    1    1    0    0    0    0    0
##   NAD    0    2    1    5    0    0    0    0    0    1    0    0    0
##   NAG    1   28    6   22    0    0   11    2    7   79    0   21    1
##   NAP    1    2    0    4    0    0    0    0    0    0    0    1    0
##   NDP    0    0    0    1    0    0    0    0    0    1    0    0    0
##   NI     0    0    0    0    0    1    0    0    0    0    0    0    0
##   NO3    2    4    0    0    0    0    1    0    0    0    0    0    0
##   PEG    1    5    0    0    0    0    0    1    0   11    0    1    0
##   PG4    0    1    0    0    0    0    0    0    0    5    0    1    1
##   PGE    0    2    1    0    0    0    0    0    0    1    0    0    1
##   PLP    0    0    2    0    0    0    0    0    0    0    0    2    0
##   PO4    2    3    0    0    3    0    0    1    0    8    0    4    2
##   SAH    0    0    1    0    0    0    1    0    0    0    0    0    0
##   SEP    0    2    0    1    0    0    1    0    0    1    0    0    0
##   SF4    0    0    0    0    0    0    0    0    1    0    0    0    0
##   SO4   74   84   16    6    5    2    4    5    0  134    1   31   29
##   TRS    0    0    0    0    0    0    0    0    0    2    0    0    0
##   ZN     1    2    2    1    5   15    0    0    0    6    0    3    3
##      
## data     K  MAN  MES   MG  MLY   MN  MPD  NAD  NAG  NAP  NDP   NI  NO3
##   1PE    0    0    0    0    2    0    0    1    4    0    0    0    0
##   ACT    0    1    2    7    2    0    1    1    6    0    2    1    2
##   ACY    0    0    0    1    1    0    0    0    0    0    0    1    0
##   ADP    0    1    0    1    1    0    0   11    2    4    0    0    0
##   ATP    0    1    1    0    0    1    0    2    4    0    1    0    0
##   BR     5    0    0    1    0    0    0    0    0    0    0    0    0
##   CA    17    2    1   40    3   28    2    0    5    2    2    6    0
##   CD     1    0    0    2    0    2    0    0    0    0    0    1    0
##   CIT    0    1    0    0    1    1    0    0    0    0    0    0    1
##   CL    42    3    1   40    1    8    3    0   14    4    0    4    2
##   CLA    0    1    0    0    0    0    0    0    2    0    0    0    0
##   COA    0    0    0    0    0    0    0    2    3    0    2    0    0
##   CU     0    0    0    1    0    1    0    0    0    0    0    1    0
##   DMS    3    0    3    1    0    1    1    0    1    3    0    2    2
##   EDO    8   16   15   29   12    3   17   11   52   12    2    0   10
##   EPE    1    0    1    2    1    0    0    0    0    0    1    0    0
##   FAD    0    0    0    0    0    0    1    7    3    3    5    0    0
##   FE     0    0    0    0    0    1    0    0    0    0    0    0    0
##   FE2    0    0    1    0    0    0    0    0    0    0    0    0    0
##   FMN    0    0    0    0    0    0    0    1    0    3    1    0    0
##   FMT    0    0    0    1    0    0    0    0    0    0    0    0    0
##   GDP    0    0    0    0    0    0    0    0    0    0    1    0    0
##   GOL    6   18   10   58   18    2   30   17   87    9    7    3    6
##   HEC    0    0    0    0    0    0    0    0    0    0    0    0    0
##   HEM    1    0    1    2    0    0    0    1    3    1    0    0    2
##   IOD    2    0    0    0    0    0    0    0    0    0    0    1    0
##   K     21    0    0    2    1    0    0    0    2    0    0    0    0
##   MAN    1    9    0    0    1    0    0    4    8    0    1    0    0
##   MES    0    0   17    0    1    0    1    0    1    0    0    0    0
##   MG     3    3    6  191    5    3    0    2   12    2    0    1    1
##   MLY    0    0    1    4    9    0    0    0    3    2    1    0    0
##   MN     1    0    0    4    0   20    0    0    1    1    0    2    0
##   MPD    0    1    0    0    0    1    3    1    2    0    0    0    0
##   NAD    0    0    1    1    2    0    0   57    6   13    4    0    0
##   NAG    3   24    8   18   10    5    4   17  551   14    8    2    2
##   NAP    0    1    0    0    0    0    0    1    1   43   11    0    0
##   NDP    0    0    0    0    0    0    0    4    1    4   10    0    0
##   NI     0    0    0    0    0    2    0    0    0    0    0    2    0
##   NO3    0    0    1    1    0    1    1    0    0    0    0    0    2
##   PEG    1    0    0    1    1    2    0    2    5    1    0    1    0
##   PG4    0    0    0    1    0    0    0    0    1    0    0    0    1
##   PGE    0    0    1    0    0    0    0    1    2    0    0    0    0
##   PLP    0    0    0    0    0    1    0    0    0    0    0    0    0
##   PO4    2    0    3    6    2    2    2    1    1    2    0    4    1
##   SAH    0    0    0    1    0    0    0    3    1    0    0    0    0
##   SEP    0    1    0    3    0    0    0    0    1    0    0    1    0
##   SF4    0    0    0    0    0    0    0    0    0    0    0    0    0
##   SO4   26    9   16   68   12   39   13    3   41    5    8   16   22
##   TRS    0    1    0    0    0    0    0    0    0    0    0    0    0
##   ZN     1    1    1   10    2   24    1    0    7    1    2   17    1
##      
## data   PEG  PG4  PGE  PLP  PO4  SAH  SEP  SF4  SO4  TRS   ZN
##   1PE    6    7    3    0    0    0    0    0    4    0    1
##   ACT    2    0    0    0    4    0    0    0   10    0    4
##   ACY    0    0    0    0    0    0    0    0    3    0    3
##   ADP    1    0    0    1    1    2    1    0    3    0    2
##   ATP    0    0    0    1    0    2    1    0    0    0    2
##   BR     0    0    0    0    0    0    0    0    1    0    1
##   CA     0    0    1    0    4    0    1    0   53    0   47
##   CD     0    0    0    0    1    0    0    0    4    0    3
##   CIT    0    0    0    0    1    0    0    0    3    0    0
##   CL     8    2    2    0   10    1    2    2   70    2   12
##   CLA    0    0    0    0    0    0    0    0    1    0    1
##   COA    0    0    1    1    0    0    0    0    1    0    0
##   CU     0    0    0    0    0    0    0    0    0    0    9
##   DMS    1    3    0    0    3    0    0    0   22    0    4
##   EDO   46   18   13    0   22    4    1    0  100    5   14
##   EPE    0    0    0    0    0    1    1    0    1    0    1
##   FAD    0    1    0    0    0    0    0    0    2    0    1
##   FE     0    0    0    0    0    0    0    0    0    0    1
##   FE2    0    0    0    0    0    0    0    0    0    0    1
##   FMN    0    0    0    0    0    0    0    0    0    0    0
##   FMT    0    0    0    0    0    1    0    0    4    0    0
##   GDP    0    0    0    0    1    1    0    0    0    0    0
##   GOL   40   24   13    2   21    2    5    0  149   19   23
##   HEC    0    0    0    0    1    0    0    0    0    0    0
##   HEM    2    0    1    0    3    0    3    0    5    0    2
##   IOD    0    0    0    0    3    1    1    0    7    0    4
##   K      0    0    0    0    0    0    0    0    2    0    1
##   MAN    0    1    0    0    0    0    0    0    2    0    0
##   MES    0    0    0    2    0    0    2    0    2    0    0
##   MG     0    2    1    0    7    0    0    2   24    8    8
##   MLY    1    2    0    0    1    0    0    0    3    0    2
##   MN     0    0    0    0    3    0    0    1    5    0   12
##   MPD    1    1    0    0    0    0    0    0    1    0    0
##   NAD    0    1    0    0    0    1    0    0    5    0    1
##   NAG   22   21    8    4    8    9    4    0   25    2   18
##   NAP    0    1    0    1    0    0    0    0    0    0    0
##   NDP    0    0    0    0    0    0    0    0    0    0    0
##   NI     0    0    0    1    0    0    0    0    0    1    2
##   NO3    0    0    0    0    0    0    0    0    3    0    1
##   PEG    0    5    1    0    2    1    1    0    1    0    1
##   PG4    4    4    2    0    0    0    0    0    2    0    1
##   PGE    0    0    1    0    0    0    0    0    0    0    0
##   PLP    0    0    0   24    2    0    0    0    2    0    3
##   PO4    1    0    0    2   25    0    1    0   37    0    2
##   SAH    0    0    0    1    0   19    0    0    0    0    0
##   SEP    0    0    0    0    0    0   15    0    1    0    2
##   SF4    0    0    0    0    0    0    0   52    0    0    0
##   SO4   10    3    2   12  195    3    7    0 1220    8   64
##   TRS    0    0    0    0    0    0    0    0    0    4    0
##   ZN     0    2    0    0    6    0    4    1   16    1  356
## 
## Overall Statistics
##                                         
##                Accuracy : 0.438         
##                  95% CI : (0.429, 0.447)
##     No Information Rate : 0.1531        
##     P-Value [Acc > NIR] : < 2.2e-16     
##                                         
##                   Kappa : 0.388         
##  Mcnemar's Test P-Value : NA            
## 
## Statistics by Class:
## 
##                      Class: 1PE Class: ACT Class: ACY Class: ADP
## Sensitivity           0.1506849   0.126697  0.0270270   0.303922
## Specificity           0.9966515   0.990956  0.9984544   0.995008
## Pos Pred Value        0.2200000   0.212121  0.1000000   0.348315
## Neg Pred Value        0.9946872   0.983345  0.9938462   0.993896
## Prevalence            0.0062287   0.018857  0.0063140   0.008703
## Detection Rate        0.0009386   0.002389  0.0001706   0.002645
## Detection Prevalence  0.0042662   0.011263  0.0017065   0.007594
## Balanced Accuracy     0.5736682   0.558826  0.5127407   0.649465
##                      Class: ATP Class: BR Class: CA Class: CD Class: CIT
## Sensitivity            0.300000 0.1309524   0.47330  0.227723  0.0943396
## Specificity            0.997425 0.9984531   0.96790  0.997418  0.9990572
## Pos Pred Value         0.411765 0.3793103   0.48094  0.433962  0.3125000
## Neg Pred Value         0.995801 0.9937559   0.96693  0.993314  0.9958988
## Prevalence             0.005973 0.0071672   0.05913  0.008618  0.0045222
## Detection Rate         0.001792 0.0009386   0.02799  0.001962  0.0004266
## Detection Prevalence   0.004352 0.0024744   0.05819  0.004522  0.0013652
## Balanced Accuracy      0.648712 0.5647027   0.72060  0.612570  0.5466984
##                      Class: CL Class: CLA Class: COA Class: CU Class: DMS
## Sensitivity            0.53468   0.700000   0.042857 0.1369863   0.366255
## Specificity            0.95296   0.999487   0.998712 0.9980252   0.991984
## Pos Pred Value         0.45203   0.777778   0.166667 0.3030303   0.491713
## Neg Pred Value         0.96578   0.999230   0.994274 0.9946094   0.986654
## Prevalence             0.06766   0.002560   0.005973 0.0062287   0.020734
## Detection Rate         0.03618   0.001792   0.000256 0.0008532   0.007594
## Detection Prevalence   0.08003   0.002304   0.001536 0.0028157   0.015444
## Balanced Accuracy      0.74382   0.849743   0.520785 0.5675058   0.679120
##                      Class: EDO Class: EPE Class: FAD Class: FE Class: FE2
## Sensitivity             0.47112   0.206349   0.607595 0.2250000  0.1176471
## Specificity             0.90478   0.998542   0.996800 0.9994007  0.9996577
## Pos Pred Value          0.31271   0.433333   0.721805 0.5625000  0.5000000
## Neg Pred Value          0.94899   0.995723   0.994649 0.9973513  0.9974385
## Prevalence              0.08422   0.005375   0.013481 0.0034130  0.0029010
## Detection Rate          0.03968   0.001109   0.008191 0.0007679  0.0003413
## Detection Prevalence    0.12688   0.002560   0.011348 0.0013652  0.0006826
## Balanced Accuracy       0.68795   0.602445   0.802197 0.6122003  0.5586524
##                      Class: FMN Class: FMT Class: GDP Class: GOL
## Sensitivity            0.523077  0.0806452   0.380000    0.41873
## Specificity            0.999056  0.9981987   0.998715    0.88950
## Pos Pred Value         0.755556  0.1923077   0.558824    0.31131
## Neg Pred Value         0.997345  0.9951257   0.997347    0.92769
## Prevalence             0.005546  0.0052901   0.004266    0.10657
## Detection Rate         0.002901  0.0004266   0.001621    0.04462
## Detection Prevalence   0.003840  0.0022184   0.002901    0.14334
## Balanced Accuracy      0.761067  0.5394219   0.689357    0.65412
##                      Class: HEC Class: HEM Class: IOD Class: K Class: MAN
## Sensitivity           0.2121212    0.58556    0.38119 0.144828  0.0957447
## Specificity           0.9994010    0.99374    0.99522 0.997235  0.9972475
## Pos Pred Value        0.5000000    0.75517    0.58333 0.396226  0.2195122
## Neg Pred Value        0.9977789    0.98644    0.98921 0.989372  0.9927220
## Prevalence            0.0028157    0.03191    0.01724 0.012372  0.0080205
## Detection Rate        0.0005973    0.01869    0.00657 0.001792  0.0007679
## Detection Prevalence  0.0011945    0.02474    0.01126 0.004522  0.0034983
## Balanced Accuracy     0.6057611    0.78965    0.68821 0.571032  0.5464961
##                      Class: MES Class: MG Class: MLY Class: MN Class: MPD
## Sensitivity            0.186813   0.38431  0.1022727  0.135135   0.037500
## Specificity            0.998108   0.98280  0.9979367  0.995334   0.998540
## Pos Pred Value         0.435897   0.49740  0.2727273  0.270270   0.150000
## Neg Pred Value         0.993665   0.97301  0.9932404  0.989009   0.993419
## Prevalence             0.007765   0.04241  0.0075085  0.012628   0.006826
## Detection Rate         0.001451   0.01630  0.0007679  0.001706   0.000256
## Detection Prevalence   0.003328   0.03276  0.0028157  0.006314   0.001706
## Balanced Accuracy      0.592461   0.68355  0.5501047  0.565234   0.518020
##                      Class: NAD Class: NAG Class: NAP Class: NDP Class: NI
## Sensitivity            0.380000    0.66146   0.333333  0.1449275 0.0303030
## Specificity            0.995333    0.95279   0.997757  0.9987984 0.9993135
## Pos Pred Value         0.513514    0.51737   0.623188  0.4166667 0.2000000
## Neg Pred Value         0.991989    0.97353   0.992619  0.9949555 0.9945346
## Prevalence             0.012799    0.07108   0.011007  0.0058874 0.0056314
## Detection Rate         0.004863    0.04701   0.003669  0.0008532 0.0001706
## Detection Prevalence   0.009471    0.09087   0.005887  0.0020478 0.0008532
## Balanced Accuracy      0.687666    0.80713   0.665545  0.5718630 0.5148083
##                      Class: NO3 Class: PEG Class: PG4 Class: PGE
## Sensitivity           0.0363636   0.000000  0.0408163  2.041e-02
## Specificity           0.9986284   0.995421  0.9980210  9.991e-01
## Pos Pred Value        0.1111111   0.000000  0.1481481  9.091e-02
## Neg Pred Value        0.9954709   0.987572  0.9919610  9.959e-01
## Prevalence            0.0046928   0.012372  0.0083618  4.181e-03
## Detection Rate        0.0001706   0.000000  0.0003413  8.532e-05
## Detection Prevalence  0.0015358   0.004522  0.0023038  9.386e-04
## Balanced Accuracy     0.5174960   0.497711  0.5194187  5.098e-01
##                      Class: PLP Class: PO4 Class: SAH Class: SEP
## Sensitivity            0.461538   0.077160   0.395833   0.300000
## Specificity            0.998800   0.990523   0.998372   0.998372
## Pos Pred Value         0.631579   0.187970   0.500000   0.441176
## Neg Pred Value         0.997603   0.974195   0.997518   0.997005
## Prevalence             0.004437   0.027645   0.004096   0.004266
## Detection Rate         0.002048   0.002133   0.001621   0.001280
## Detection Prevalence   0.003242   0.011348   0.003242   0.002901
## Balanced Accuracy      0.730169   0.533842   0.697103   0.649186
##                      Class: SF4 Class: SO4 Class: TRS Class: ZN
## Sensitivity            0.896552     0.6800  0.0800000   0.58361
## Specificity            0.999657     0.8647  0.9996572   0.97768
## Pos Pred Value         0.928571     0.4760  0.5000000   0.58940
## Neg Pred Value         0.999486     0.9373  0.9960724   0.97715
## Prevalence             0.004949     0.1531  0.0042662   0.05205
## Detection Rate         0.004437     0.1041  0.0003413   0.03038
## Detection Prevalence   0.004778     0.2187  0.0006826   0.05154
## Balanced Accuracy      0.948104     0.7724  0.5398286   0.78064